The Stealth Cruisers with their stealth ability and beam weapons, especially layout B with its powerful Glaive Beam bear a similarity to Shadow Ships, which would appear out of nowhere and destroy any ship of the younger races with a single blast from its only weapon, a red beam weapon.

Lanius ships, especially the non player ones, look very similar to Shadow Ships in its shape.

In a random mission, you will come to a station and when asking to refuel, the station's respond will be, "Go away! We don't serve your kind here! (Star Wars Episode IV: A New Hope, during the cantina scene, a quote from the bartender to R2-D2 and C-3PO)

If you run out of fuel and wait, one of the ships that finds you is described as a modified YT-1300 Freighter obviously used for smuggling. This is a reference to the Millennium Falcon.

Notch, the developer of Minecraft. This is because when the game was being funded on Kickstarter, the first 100 people to donate $100 or more had their name added to the crew roster, and Notch was one of these people.

GMFaux, another Kickstarter donator.

Mike Weston, the burned (fired) spy from the American TV show Burn Notice.

Ohm (shortened form of Ohmwrecker), the YouTube Let's Player who, on camera, beat the supposedly impossible boss in the final sector (sector 2) in the alpha version of the game.

The Kestrel Cruiser is a reference to the Escape Velocity series by Ambrosia. Also a spacefaring simulator, The Kestrel is the popular and most powerful civilian ship available in Escape Velocity and returns as a powerful endgame ship in Escape Velocity: Nova available upon game completion.

Layout B of the Rock Cruiser (Shivan) is possibly named after the Shivan race in the game Freespace. The color scheme is evidence of this, although the Shivan race in that game utilizes more shielding than armor, in contrast to the Rock ships. (Not entirely true. Note: Shivan bombers have enormous amount of armor plating, especially the Nephilim class which is really hard to shoot down with shields down, even with missiles)

Layout A of the Crystal Cruiser (Bravais) is named after a Bravais lattice - a mathematical method of describing/representing a crystal structure and the points within it.

Layout B of the Zoltan ship (Noether) is named for Emmy Noether, a groundbreaking mathematician and physicist.

The Nesasio is probably designed after Mass Effect's SSV Normandy, as both are stealth-themed ships, share a similar delta form, and have similar room layouts (FTL's being a simpler version).

The Shrike could also be a reference to the almost mythical mechanical terror from Dan Simmon's Hyperion cantos, especially considering the resemblance between it and the Lanius. Shrike is also a killer robot in book Mortal Engines, and it has knife-like claws in both its hands.

Theseus (Mantis C) was the mythical founder of Athens; furthermore, the eponymous Ship of Theseus refers to a ship which had all of its parts replaced, but still considered the same ship - a situation which is bound to happen to your boarding party, as the ship is outfitted with a clone bay.